Abstract
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.
Highlights
About three quarters of the human genome could be transcribed into RNA, including 4,693 miRNAs [1] and 105,255 long noncoding RNAs [2]
The similarity of the monomers was measured by the sequence alignment and by the structure alignments
Sequence and structure alignment approaches were compared in template-based modeling of protein-RNA complexes
Summary
About three quarters of the human genome could be transcribed into RNA, including 4,693 miRNAs [1] and 105,255 long noncoding RNAs [2]. High-throughput experimental techniques (HITS-CLIP [7], PAR-clip [8], RIP-chip [9]) and computational methods [10,11,12,13,14,15,16,17,18] have been developed to characterize protein-RNA interactome. These methods identify and characterize protein-RNA interactions, but do not provide the structure of protein-RNA complexes, which is important for understanding the molecular function. This gap has to be filled by computational approaches [19]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
